Reference: A reference is a canonical assembled DNA sequence, intended to act as a reference coordinate space for other genomic annotations. A single reference might represent the human chromosome 1 or mitochandrial DNA, for instance. A reference belongs to one or more reference sets. For more genomics resource definitions, see [Fundamentals of Google Genomics]( omics)

Reference is referenced in 1 repository


func (s *Range) MarshalJSON() ([]byte, error) {
	type noMethod Range
	raw := noMethod(*s)
	return gensupport.MarshalJSON(raw, s.ForceSendFields, s.NullFields)

// Read: A read alignment describes a linear alignment of a string of
// DNA to a reference sequence, in addition to metadata about the
// fragment (the molecule of DNA sequenced) and the read (the bases
// which were read by the sequencer). A read is equivalent to a line in
// a SAM file. A read belongs to exactly one read group and exactly one
// read group set. For more genomics resource definitions, see
// [Fundamentals of Google
// Genomics](
// omics) ### Reverse-stranded reads Mapped reads (reads having a
// non-null `alignment`) can be aligned to either the forward or the
// reverse strand of their associated reference. Strandedness of a
// mapped read is encoded by `alignment.position.reverseStrand`. If we
// consider the reference to be a forward-stranded coordinate space of
// `[0, reference.length)` with `0` as the left-most position and
// `reference.length` as the right-most position, reads are always
// aligned left to right. That is, `alignment.position.position` always
// refers to the left-most reference coordinate and `alignment.cigar`
// describes the alignment of this read to the reference from left to
// right. All per-base fields such as `alignedSequence` and
// `alignedQuality` share this same left-to-right orientation; this is
// true of reads which are aligned to either strand. For
// reverse-stranded reads, this means that `alignedSequence` is the
// reverse complement of the bases that were originally reported by the
// sequencing machine. ### Generating a reference-aligned sequence
// string When interacting with mapped reads, it's often useful to
// produce a string representing the local alignment of the read to
// reference. The following pseudocode demonstrates one way of doing
// this: out = "" offset = 0 for c in read.alignment.cigar { switch
// c.operation { case "ALIGNMENT_MATCH", "SEQUENCE_MATCH",
// read.alignedSequence[offset:offset+c.operationLength] offset +=
// c.operationLength break case "CLIP_SOFT", "INSERT": offset +=
// c.operationLength break case "PAD": out += repeat("*",
// c.operationLength) break case "DELETE": out += repeat("-",